 
####################################################### 
#                                                     # 
#                        ACE                          # 
#                                                     # 
#        Ab-initio protein structure prediction       # 
#                         &                           # 
#               Comparative modeling                  # 
#                                                     # 
#                     Evaluator                       # 
#                                                     # 
#                ----------------- 11/1998            # 
#                                                     # 
#                         by                          # 
#           Adam Zemla & Ceslovas Venclovas           # 
#                                                     # 
#         Protein Structure Prediction Center         # 
#      Lawrence Livermore National Laboratory, CA     # 
#                                                     # 
####################################################### 
########################## 
#                        # 
#    ACE parameters:     # 
#                        # 
########################## 
# 
CONANA-INTER           ../CONANA/T0047.inter 
# 
NUMBER-OF-PARENTS      4 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0047.1mup.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0047.1obp_A.rot 
ALIGNMENT-DALI(3)      ../PARENTS/casp3.T0047.1beb_A.rot 
ALIGNMENT-DALI(4)      ../PARENTS/casp3.T0047.1epa_B.rot 
# 
ITER-CUTOFF            2.5       #    DISTANCE cutoff (for CA (iter))  
# 
# 
# MEASURES: 
# 
# For AB: 0 3 9 13 14 
# For CM: 0 1 2 3 6 7 8 9 10 11 12 13 14 18 
# 
ARMSMC  0 1 2     7 8 9    11 12 13 14 18 
ARMSSC  0 1 2 3 6 7 8 9    11 12 13 14 18 
# 
CRMSCA  0 1 2     7 8 9 10 11 12 13 14 18 
CRMSMC  0 1 2     7 8 9 10 11 12 13 14 18 
CRMSSC  0 1 2 3 6     9    11 12 13 14 18 
CRMSALL 0 1 2     7 8 9    11 12 13 14 18 
# 
D-E_CA  0 1 2     7 8 9    11 12 13 14 18 
D-E_MC  0 1 2     7 8 9    11 12 13 14 18 
D-E_SC  0 1 2 3 6 7 8 9    11 12 13 14 18 
D-E_ALL 0 1 2     7 8 9    11 12 13 14 18 
# 
# Output parameters 
# 
DIHED-OUTPUT        0         #    1 - ON, 0 - OFF 
SS-OUTPUT           0         #    1 - ON, 0 - OFF  
PHI-PSI             0         #    1 - SEPARATELY, 0 - NO  
ALIGNMENT-OUTPUT    0         #    1 - ON, 0 - OFF 
# 
# Calculation parameters 
# 
TEMP-FACTOR         30.0      #    Target structure temperature factor cutoff  
ACCESS-CUTOFF       0.20      #    Solvent accessibility cutoff  
ANGLES-CORRECT      30.0      #    target-model  (diff < 30.0)  
ROTAMERS-LIMIT      30.0      #    target-parent (diff > 30.0) 
SC-SWAPPING         1         #    1 - ON, 0 - OFF  
DSSP-HELIX          6         #    Secondary Structure subset: helix cutoff  
DSSP-STRAND         3         #    Secondary Structure subset: strand cutoff 
LIGAND-DIST1        4.0       #    Ligand contact: contact with ligand cutoff 
LIGAND-DIST2        6.0       #    Ligand contact: protein neighborhood cutoff 
PARENT-DIST3        2.5       #    target-parent (dist > 2.5) 
# 
CRMS-METHOD         3         #    0 - ALL, 1 - CA, 2 - MC+CB, 3 - CA (iter)  
# 
########################## 
#                        # 
#      ACE results:      # 
#                        # 
########################## 
 
# Reading the coordinates set (1) 
 
 
# Evaluating the coordinates set (1) 
 
# WARNING! TARGET 1287 atoms, MODEL 1611 atoms, 1287 common with TARGET 
           Number of atoms possible to evaluate: 1279 
 
 
 CA-RMS TARGET<->PARENT(1mup)	 1.202822 
 
 CA-RMS TARGET<->PARENT(1obp-A)	 2.128074 
 
 CA-RMS TARGET<->PARENT(1beb-A)	 2.195152 
 
 CA-RMS TARGET<->PARENT(1epa-B)	 1.899896 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    35.59           84.6   312    99.4   314     ARMSMC  
     WELL ORDERED  . . . . .    21.27           90.5   190   100.0   190     ARMSMC  
     NO INTER CONTACTS . . .    34.02           86.0   292    99.3   294     ARMSMC  
     SHIFTED CHAIN . . . . .    60.84           60.7    61    96.8    63     ARMSMC  
     ALTERNATIVE PARENT  . .    58.39           42.9    14   100.0    14     ARMSMC  
     SECONDARY STRUCTURE . .    16.86           92.0   162   100.0   162     ARMSMC  
     LARGE SHIFTS/INSERTIONS    87.15           38.1    21    95.5    22     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    44.18           77.9   163    99.4   164     ARMSMC  
     BURIED  . . . . . . . .    22.73           91.9   149    99.3   150     ARMSMC  
     CORE  . . . . . . . . .    28.46           88.0   291    99.7   292     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    72.17           57.1   140    99.3   141     ARMSSC1 
     WELL ORDERED  . . . . .    60.46           67.8    59   100.0    59     ARMSSC1 
     NO INTER CONTACTS . . .    71.86           56.9   130    99.2   131     ARMSSC1 
     RELIABLE SIDE CHAINS  .    69.69           58.0   131    99.2   132     ARMSSC1 
     CHANGED ANGLES  . . . .    89.39           32.3    65   100.0    65     ARMSSC1 
     SHIFTED CHAIN . . . . .    94.11           29.6    27    96.4    28     ARMSSC1 
     ALTERNATIVE PARENT  . .   101.69           20.0     5   100.0     5     ARMSSC1 
     SECONDARY STRUCTURE . .    63.05           62.7    75   100.0    75     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    87.04           22.2     9   100.0     9     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    85.38           40.8    76    98.7    77     ARMSSC1 
     BURIED  . . . . . . . .    52.30           76.6    64   100.0    64     ARMSSC1 
     CORE  . . . . . . . . .    71.03           59.5   131    99.2   132     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    67.20           53.6   110    99.1   111     ARMSSC2 
     WELL ORDERED  . . . . .    53.73           77.3    44   100.0    44     ARMSSC2 
     NO INTER CONTACTS . . .    65.01           56.9   102    99.0   103     ARMSSC2 
     RELIABLE SIDE CHAINS  .    63.96           57.1    84   100.0    84     ARMSSC2 
     CHANGED ANGLES  . . . .    74.10           44.4    63    98.4    64     ARMSSC2 
     SHIFTED CHAIN . . . . .    72.64           36.8    19    95.0    20     ARMSSC2 
     ALTERNATIVE PARENT  . .    51.64           40.0     5   100.0     5     ARMSSC2 
     SECONDARY STRUCTURE . .    60.95           66.1    59   100.0    59     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    65.81           28.6     7   100.0     7     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    77.29           39.7    63    98.4    64     ARMSSC2 
     BURIED  . . . . . . . .    50.61           72.3    47   100.0    47     ARMSSC2 
     CORE  . . . . . . . . .    67.30           55.3   103    99.0   104     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    67.61           44.2    43   100.0    43     ARMSSC3 
     WELL ORDERED  . . . . .    43.61           42.9     7   100.0     7     ARMSSC3 
     NO INTER CONTACTS . . .    68.38           42.1    38   100.0    38     ARMSSC3 
     RELIABLE SIDE CHAINS  .    65.97           46.3    41   100.0    41     ARMSSC3 
     CHANGED ANGLES  . . . .    70.46           37.1    35   100.0    35     ARMSSC3 
     SHIFTED CHAIN . . . . .    65.70           46.2    13   100.0    13     ARMSSC3 
     ALTERNATIVE PARENT  . .    93.89            0.0     3   100.0     3     ARMSSC3 
     SECONDARY STRUCTURE . .    80.40           30.0    20   100.0    20     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    93.42           20.0     5   100.0     5     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    69.96           42.4    33   100.0    33     ARMSSC3 
     BURIED  . . . . . . . .    59.17           50.0    10   100.0    10     ARMSSC3 
     CORE  . . . . . . . . .    63.43           47.4    38   100.0    38     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    82.68           40.9    22   100.0    22     ARMSSC4 
     WELL ORDERED  . . . . .    75.55           50.0     4   100.0     4     ARMSSC4 
     NO INTER CONTACTS . . .    85.37           38.9    18   100.0    18     ARMSSC4 
     RELIABLE SIDE CHAINS  .    82.68           40.9    22   100.0    22     ARMSSC4 
     CHANGED ANGLES  . . . .    88.21           36.8    19   100.0    19     ARMSSC4 
     SHIFTED CHAIN . . . . .    73.80           57.1     7   100.0     7     ARMSSC4 
     ALTERNATIVE PARENT  . .    77.29            0.0     1   100.0     1     ARMSSC4 
     SECONDARY STRUCTURE . .    88.68           40.0    10   100.0    10     ARMSSC4 
     LARGE SHIFTS/INSERTIONS    83.38           33.3     3   100.0     3     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    86.54           35.3    17   100.0    17     ARMSSC4 
     BURIED  . . . . . . . .    67.92           60.0     5   100.0     5     ARMSSC4 
     CORE  . . . . . . . . .    82.57           42.1    19   100.0    19     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.70807     r(1,2) =   0.68702     r(1,3) =   0.16324 
 r(2,1) =  -0.70440     r(2,2) =   0.70343     r(2,3) =   0.09492 
 r(3,1) =  -0.04962     r(3,2) =  -0.18219     r(3,3) =   0.98201 
THE OFFSET VECTOR: 
 v(1) =  41.44157     v(2) =  20.83002     v(3) =  -6.22188 
 
 Number of iteration 25                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   0.73           (Number of atoms:  144) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    1.38        157    99.4   158     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0088                            CRMSCA  
     WELL ORDERED  . . . . .    0.74         95   100.0    95     CRMSCA  
     NO INTER CONTACTS . . .    1.35        147    99.3   148     CRMSCA  
     SHIFTED CHAIN . . . . .    2.93         31    96.9    32     CRMSCA  
     ALTERNATIVE PARENT  . .    4.41          7   100.0     7     CRMSCA  
     SECONDARY STRUCTURE . .    0.61         81   100.0    81     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    4.32         11   100.0    11     CRMSCA  
     SURFACE . . . . . . . .    1.75         82    98.8    83     CRMSCA  
     BURIED  . . . . . . . .    0.81         75   100.0    75     CRMSCA  
     CORE  . . . . . . . . .    0.81        146    99.3   147     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    1.44        774    99.4   779     CRMSMC  
     WELL ORDERED  . . . . .    0.72        453   100.0   453     CRMSMC  
     NO INTER CONTACTS . . .    1.41        724    99.3   729     CRMSMC  
     SHIFTED CHAIN . . . . .    3.00        151    96.8   156     CRMSMC  
     ALTERNATIVE PARENT  . .    4.44         33   100.0    33     CRMSMC  
     SECONDARY STRUCTURE . .    0.69        402   100.0   402     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    4.41         53   100.0    53     CRMSMC  
     SURFACE . . . . . . . .    1.81        406    98.8   411     CRMSMC  
     BURIED  . . . . . . . .    0.87        368   100.0   368     CRMSMC  
     CORE  . . . . . . . . .    0.90        721    99.3   726     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    2.49        651    99.4   655     CRMSSC  
     WELL ORDERED  . . . . .    1.65        321   100.0   321     CRMSSC  
     NO INTER CONTACTS . . .    2.42        602    99.3   606     CRMSSC  
     RELIABLE SIDE CHAINS  .    2.48        571    99.7   573     CRMSSC  
     CHANGED ANGLES  . . . .    3.27        305    99.3   307     CRMSSC  
     SECONDARY STRUCTURE . .    1.96        357   100.0   357     CRMSSC  
     LARGE SHIFTS/INSERTIONS    5.40         42   100.0    42     CRMSSC  
     SURFACE . . . . . . . .    3.12        356    98.9   360     CRMSSC  
     BURIED  . . . . . . . .    1.40        295   100.0   295     CRMSSC  
     CORE  . . . . . . . . .    2.15        609    99.3   613     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    2.03       1279    99.4  1287     CRMSALL 
     WELL ORDERED  . . . . .    1.24        701   100.0   701     CRMSALL 
     NO INTER CONTACTS . . .    1.97       1190    99.3  1198     CRMSALL 
     SHIFTED CHAIN . . . . .    3.63        238    96.7   246     CRMSALL 
     ALTERNATIVE PARENT  . .    4.88         51   100.0    51     CRMSALL 
     SECONDARY STRUCTURE . .    1.49        681   100.0   681     CRMSALL 
     LARGE SHIFTS/INSERTIONS    4.87         86   100.0    86     CRMSALL 
     SURFACE . . . . . . . .    2.56        684    98.8   692     CRMSALL 
     BURIED  . . . . . . . .    1.15        595   100.0   595     CRMSALL 
     CORE  . . . . . . . . .    1.65       1193    99.3  1201     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     5.15      4   100.0     4      60-ENGE-63   
 CA  LOOP  2     3.74      5   100.0     5     153-KTDRC-157  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     5.16     19   100.0    19      60-ENGE-63   
 MC  LOOP  2     3.92     25   100.0    25     153-KTDRC-157  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     5.52     30   100.0    30      60-ENGE-63   
 ALL LOOP  2     4.53     41   100.0    41     153-KTDRC-157  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     0.28      4   100.0     4      60-ENGE-63   
 CA  LOOP  2     1.69      5   100.0     5     153-KTDRC-157  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     0.65     19   100.0    19      60-ENGE-63   
 MC  LOOP  2     2.12     25   100.0    25     153-KTDRC-157  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     1.93     30   100.0    30      60-ENGE-63   
 ALL LOOP  2     3.23     41   100.0    41     153-KTDRC-157  
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.593      0.341       0.210    157    99.4   158     ERRCA  
     WELL ORDERED  . . . . .    0.287      0.263       0.187     95   100.0    95     ERRCA  
     NO INTER CONTACTS . . .    0.559      0.332       0.203    147    99.3   148     ERRCA  
     SHIFTED CHAIN . . . . .    2.074      0.635       0.318     31    96.9    32     ERRCA  
     ALTERNATIVE PARENT  . .    3.780      0.796       0.398      7   100.0     7     ERRCA  
     SECONDARY STRUCTURE . .    0.247      0.264       0.186     81   100.0    81     ERRCA  
     LARGE SHIFTS/INSERTIONS    3.762      0.808       0.404     11   100.0    11     ERRCA  
     SURFACE . . . . . . . .    0.858      0.408       0.251     82    98.8    83     ERRCA  
     BURIED  . . . . . . . .    0.303      0.268       0.166     75   100.0    75     ERRCA  
     CORE  . . . . . . . . .    0.354      0.306       0.196    146    99.3   147     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.637      0.359       0.217    774    99.4   779     ERRMC  
     WELL ORDERED  . . . . .    0.310      0.289       0.197    453   100.0   453     ERRMC  
     NO INTER CONTACTS . . .    0.607      0.353       0.213    724    99.3   729     ERRMC  
     SHIFTED CHAIN . . . . .    2.109      0.630       0.315    151    96.8   156     ERRMC  
     ALTERNATIVE PARENT  . .    3.762      0.783       0.392     33   100.0    33     ERRMC  
     SECONDARY STRUCTURE . .    0.292      0.288       0.196    402   100.0   402     ERRMC  
     LARGE SHIFTS/INSERTIONS    3.819      0.808       0.404     53   100.0    53     ERRMC  
     SURFACE . . . . . . . .    0.899      0.417       0.251    406    98.8   411     ERRMC  
     BURIED  . . . . . . . .    0.348      0.295       0.180    368   100.0   368     ERRMC  
     CORE  . . . . . . . . .    0.403      0.326       0.203    721    99.3   726     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.398      0.494       0.263    651    99.4   655     ERRSC  
     WELL ORDERED  . . . . .    0.841      0.432       0.240    321   100.0   321     ERRSC  
     NO INTER CONTACTS . . .    1.339      0.489       0.261    602    99.3   606     ERRSC  
     RELIABLE SIDE CHAINS  .    1.364      0.482       0.259    571    99.7   573     ERRSC  
     CHANGED ANGLES  . . . .    2.166      0.605       0.308    305    99.3   307     ERRSC  
     SHIFTED CHAIN . . . . .    3.280      0.704       0.352    114    96.6   118     ERRSC  
     ALTERNATIVE PARENT  . .    4.725      0.826       0.413     23   100.0    23     ERRSC  
     SECONDARY STRUCTURE . .    1.044      0.463       0.253    357   100.0   357     ERRSC  
     LARGE SHIFTS/INSERTIONS    4.618      0.810       0.405     42   100.0    42     ERRSC  
     SURFACE . . . . . . . .    2.016      0.589       0.307    356    98.9   360     ERRSC  
     BURIED  . . . . . . . .    0.652      0.380       0.210    295   100.0   295     ERRSC  
     CORE  . . . . . . . . .    1.176      0.472       0.253    609    99.3   613     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.013      0.425       0.239   1279    99.4  1287     ERRALL 
     WELL ORDERED  . . . . .    0.550      0.351       0.215    701   100.0   701     ERRALL 
     NO INTER CONTACTS . . .    0.968      0.419       0.236   1190    99.3  1198     ERRALL 
     SHIFTED CHAIN . . . . .    2.634      0.662       0.331    238    96.7   246     ERRALL 
     ALTERNATIVE PARENT  . .    4.187      0.802       0.401     51   100.0    51     ERRALL 
     SECONDARY STRUCTURE . .    0.676      0.374       0.224    681   100.0   681     ERRALL 
     LARGE SHIFTS/INSERTIONS    4.184      0.810       0.405     86   100.0    86     ERRALL 
     SURFACE . . . . . . . .    1.464      0.502       0.279    684    98.8   692     ERRALL 
     BURIED  . . . . . . . .    0.494      0.336       0.194    595   100.0   595     ERRALL 
     CORE  . . . . . . . . .    0.784      0.397       0.228   1193    99.3  1201     ERRALL 
 
 
 
DISTANCES: Percent of total atoms where distance (target <-> model) in global 
           superposition is less than: 1 , 2 , 3 , 5 , 10 Angstroms 
            D < 1     D < 2     D < 3     D < 5    D < 10      NP      TN 
CA  (N)       127       141       145       154       157     157     158   DISTCA 
CA  (P)     80.38     89.24     91.77     97.47     99.37             158   DISTCA 
CA  (RMS)    0.51      0.64      0.76      1.14      1.38                   DISTCA 
 
ALL (N)       809      1011      1107      1221      1279    1279    1287   DISTALL 
ALL (P)     62.86     78.55     86.01     94.87     99.38            1287   DISTALL 
ALL (RMS)    0.55      0.79      1.05      1.53      2.03                   DISTALL 
 
CA RMS: P<->T (parent <-> target), and T<->M (target <-> model) calculated using 
        CA positions for which there exists an alignment with principal parent, 
        and for which does not (LARGE SHIFTS/INSERTIONS): 
              P<->T         T<->M         T<->M (LSI) 
CA  (N)         147           146            11          RMSLSI 
CA  (P)       93.04         92.41          6.96          RMSLSI 
CA  (RMS)      0.77          0.81          4.32          RMSLSI 
 
 
 
END of the results output 
